Dear Charles and other Xplor-NIH users, I've recently switched over from CNS to Xplor-NIH and I was hoping that I could get some help refining my RNA. I plan on using NOEs, hydrogen bonds, dihedrals, weak-planarity, and several categories of RDCs measured in phage. My questions are:
1) I noticed that there is an example in the eginputs directory of an RNA refinement using orient and rama; is there a simplified example that doesn't use these, analogous to the protG example that uses "dynamics internal" rather than "dynamics torsion?" Starting from the tutorial directory I generated an input file using the old "dynamics torsion" scripting format with "soft" noe wells rather than "square," which works OK. When I switch to "square" I get the dreaded rotation matrix error as others have seen with "dynamics torsion." So presumably I'd want to switch over to "dynamics internal" but I'd prefer a more simplified example to start off with, preferably with a dynamics schedule appropriate for nucleic acids. 2) Regarding template generation, I've noticed that when I generate my RNA template structure, about 1/2 to 2/3 of all of the amino H22s, 62s or 42s, point back to the major groove face rather the the Watson-Crick face. Is there some way to fix this so that they all point to the WC face in the template? This would make using H-bond restraints derived from HNN-COSY much more easy to implement. I'm currently using topallhdg.dna and parallhdg.dna as topology and parameter files, seq2psf to generate the psf file from sequence, and adding in the axis via par_axis.pro and axis.psf during pdb construction. I've could try editing the output pdb by hand, swithing H22 and H21 coordinates, but that seems like a rather clumsy solution. I reckon that a DIHEdral statement in the topology and parameter files could fix this automatically but I'm not sure if I should edit these files, nor how really. 3) Related to 2, I renumber half of the RNA residues by hand at the psf stage (Ugh) so that the input template has a numbering analogous to its postion in the larger wild-type RNA, ie 257-272, 284-299. I know how to change the starting number when generating the psf file, but I can't seem to figure out how to restart the numbering sequence halfway allong the chain. Any assistance would be great. Thanks Tom Leeper
